How to use gubbins with bactsnp results

Question

[Molinia]

Hello everybody,

I'm trying to understand how the gubbins software works based on results obtained with bactsnp. I wanted to test with a bacterial genome, CP025268.1 (knowing that I have to do this on 10 genomes) to be precise and I used the pseudo genome created by bactsnp as input for gubbins because it can also take a FASTA alignment file. But when I run gubbins I get this error:

"Error with input FASTA file: you need more than 3 sequences to build a meaningful tree. Each sequence must have a name and some genomic data. There input alignment file does not exist or has an invalid format"

While searching I saw that my alignment file contained only one line beginning with '>' while in the test file of example gubbins there are 11 of them numbered like that:

"PMEN1.aln:>2682
PMEN1.aln:>1731
PMEN1.aln:>1788
PMEN1.aln:>3350
PMEN1.aln:>3355
PMEN1.aln:>1842
PMEN1.aln:>2097
PMEN1.aln:>2098
PMEN1.aln:>1789
PMEN1.aln:>2699
PMEN1.aln:>3267
"

PMEN1 is an S pneumoniae and the numbers are its isolates. I don't understand how to proceed with my files, I'm missing something, can you help me? Thank you in advance.

[Molinia]

Can somebody help me ?